The Elrics discover the horrific ingredient needed to create a Philosopher's Stone. When night falls, they prowl the grounds of a secret laboratory in search of more facts – but the brothers find only danger.

Full Synopsis: Plot Details Follow

Having arrived in Central City with Major Armstrong, Ed and Al are horrified to learn that the first branch of the National Central Library - where Dr. Marcoh's notes were presumably hidden - has been completely burned down. Meanwhile, back in East City, Lust explains to Gluttony that she had burned down the facility in the capital after discovering that Fullmetal had learned the whereabouts of Marcoh's notes, but her ravenous companion is preoccupied with something else - the unmistakable scent of an Ishvalan cloaked in blood. Down in the sewer tunnels, Scar is suddenly attacked by Gluttony and Lust and their battle causes an explosion.

In his office, Colonel Mustang hears a report from Lt. Hawkeye and 2nd Lt. Havoc that sightings of Scar have completely dropped off since his attack on the Elric brothers. Roy, however, hopes that the Scarred Man is still in East City, since solving a problem that even the top brass in the capital can't handle would surely earn him points with Central Command and further facilitate his secret bid for the seat of Führer and supreme military authority. As Hawkeye advises him to be more discreet with such ambitious declarations, the three receive word of the sewer explosion and head out to investigate. Riza identifies Scar's bloodstained jacket floating in the river and while Havoc asserts that no bodies have been found, Roy assigns him and his team to clearing the area and searching for Scar. Meanwhile, hiding among the amassing crowd, Gluttony laments his inability to kill and eat the Ishvalan murderer, but Lust assures him that Scar will remain inactive for a while with the injuries he sustained and states that she is returning to Central to report to "Father".

In Central, Ed is introduced to the soldiers who will be taking over the Elrics' security detail from Major Armstrong - 2nd Lt. Maria Ross and Sergeant Denny Brosh. Ross and Brosh escort the boys to meet someone who can possibly help them, a woman named Sheska who had been well-acquainted with the materials being cataloged in the library's first branch. Arriving at her house, they learn that Sheska was fired for reading the library's texts instead of doing her job and that she distinctly remembers Tim Marcoh's work being filed in the first branch. Dejected at this confirmation of their objective's destruction, Ed and Al thank Sheska and prepare to leave, but she informs them that, with her photographic memory, she could reproduce the text perfectly for them if they'd like. Five days later, the transcript is finished and, though all of what Sheska has written down appears to be no more than a standard cookbook, Edward thanks her and takes the transcripts back to the library's main branch for study. Once there, he explains to Sgt. Brosh that many alchemists code their high-level alchemical documents so as to keep their information from falling into the wrong hands; if Sheska's copy is perfect and exact, the Elrics may be able to crack the code and decipher Marcoh's secret notes after all. However, even after several hours of hard work, the Elrics make very little headway into understanding what Dr. Marcoh was working on. They are visited by Lt. Colonel Hughes, who complains about the loss of important court-martial office records that were being stored in the library's first branch, and when they inform him that Sheska (who had read those records) is capable of reproducing them all from memory, he gladly offers her a new job in his office. The boys continue their research, but become furious when, after ten days, they finally decipher the code and discover the secret that Marcoh was trying to hide - that the Philosopher's Stone's main ingredient is a live human being. Ross and Brosh are horrified, but Edward asks them to reveal this information to no one else.

That evening, Major Armstrong comes to visit the boys at their hotel, but is told by Maria Ross that the Elrics are too tired to receive visitors. Unfortunately, when she and Denny begin whispering to each other about Ed and Al's melancholy, Armstrong becomes suspicious. Up in the room, as the boys lament their rotten luck and wonder if their original forms are forever lost to them, Edward mentions to Alphonse that there is something important he always wanted to discuss with his little brother but was too afraid to bring up. However, Edward is interrupted when Major Armstrong bursts into the room, having pressured Brosh and Ross into telling him why the boys have been so glum. As Armstrong weeps over the boys' misfortune and laments how cruel the truth can be, Edward is suddenly reminded of Dr. Marcoh's cryptic final message - that there is a "truth behind the truth". Taking this to mean that there is something else yet to be discovered, Edward resumes his investigation with the help of the others. Looking at a city map which denotes all of the four Alchemical Laboratories currently being operated in Central City, Edward notes a supposedly abandoned Fifth Laboratory within the city limits and proposes that this site is most likely the facility at which Philosopher's Stones were being manufactured - citing its adjacence to Central Prison as a key, since death row inmates could conceivably have been used as the Stone's necessary "live ingredients" without attracting attention. Fearing the political ramifications if the central government is involved in such an undertaking, Armstrong prepares to investigate the matter quietly on his own, advising Brosh and Ross not to speak of this to anyone and demanding that the Elric brothers remain in their hotel and keep away from Lab 5 until further notice.

Under cover of night, however, the boys sneak away to investigate the facility - curiously discovering that a soldier has been placed outside as a guard despite the building being supposedly "abandoned". Realizing that the only covert way into the lab is through the narrow vent system, Edward opts to head inside while Alphonse remains without. Deep within the recesses of the empty lab, two armor-clad, shadowy figures calling each other 48 and 66 sense the intruders and stir; 66 makes plans to go after Al while 48 prepares to take Edward on. Noticing that the facility still has electricity being fed to its lighted hallways, Ed confirms that the lab is still in use. Meanwhile, Alphonse is suddenly attacked by 66.

This is the first episode of the 2009 series to depict the serious, yet negligible, injury of a Homunculus when Scar transmutes off Gluttony's left arm. In the manga and 2003 anime, that honor is given to Tim Marcoh's attack on Lust.

When Maes Hughes visits the Elric brothers, we are given our first 2009 series glimpse of the push knife he has sheathed at his back.

During their discussion about Lab 5, all references to Basque Grand are removed from this episode. Additionally, while Edward is reminded of Marcoh's words by a comment from Denny Brosh in the manga, it is Alex Armstrong who jogs his memory in this episode.

Instead of going to another library and learning about Sheska from the other librarians, the Elrics head straight for Sheska's house, with Maria Ross filling the boys in about Sheska's background.